Pokemon XY&Z: Saving Kalos from the wrath of Zygarde
by Ren5819
Summary: Team Flare manages to kidnap Zygarde core squishy and take it to a destination unknown to our heroes. As Ash & team try to trace it, we uncover more intriguing details about mega evolutions and the powers of the legendary trios. Can they save Squishy in time? contains anime references
1. Beginnings: A beautiful day :)

**A/N Hi.. I wrote this for my own amusement.. I'm not a professional writer at all. One day I was bursting with pent up creativity, I like pokemon and the plot just came to me. Do let me know if you like it in comments section :)**

 **As for characters, I have tried to be as true to the anime as possible. The only change is that Serena is a little stronger. I didn't like that anime made her look kind of helpless. My Serena is strong enough to be of help for Ash in face of trouble.**

 **Also, although I have explored her feelings for Ash a little, it is not a love story. Another change is that she has a female Kirlia instead of Pancham.**

 **Disclaimer: I do not own pokemon or any of the cool stuff about them.**

 **Spoiler alert for dub viewers: I have a personal preference for Japanese version of the anime, which is always few episodes ahead of dubbed version. My story may contain details from episodes that haven't been dubbed yet.**

* * *

 **Ready here we go! In this chapter, we meet Ash training for Kalos league with Clemont and Serena. There's a cute Ash vs Serena battle in between. On the other hand, Team Flare has internal discords..**

* * *

After a chilling rematch in snowbelle gym, Ash just got himself the icerberg badge. The blond siblings, Clemont and Bonnie articulated their excitement at the win but a certain blue eyed girl was standing still, looking steadily at Ash as she breathed heavily. _Welcome back... welcome back Ash_ Serena thought, her smile bright due to Ash's victory against snowbelle gym leader wulfric and his mega abomasnow. Pikachu, talonflame and greninja had done it.

"Congratulations Ash!"

"The Ash greninja form was truly something to see!"

"Don't forget pikachu and talonflame guys!.." Exclaimed Bonnie supported by Dedene. Squishy was hiding in her bag since they were not alone.

As Serena and Clemont celebrated, they all tried to forget the awkward time when Ash walked away from them, upset after his crushing defeat at the gym when he challenged Wulfric for the first time. Ash was thinking along the same lines.

"Listen um Serena, thank you.. for that day, you know when I..." Ash wasn't a emotional person. He didn't know how to express them.

"Oh.." Serena blushed deep pink under Ash's gaze. It was no secret that she had a crush on him. She made an effort to check her fluttering heartbeat and put on a normal smile.

"Congratulations Ash"

 **Meanwhile at Team Flare HQ**

"The core is responding to something unknown. It's producing energy." Said a tomboyish scientist with green shoulder length hair. This was Bryony.

"It's quite a sight but again I always knew what Zygarde core is worth", said orange haired Aliana snidely. Rivalry between the two young scientists was apparent.

"Oh ho ho.. Just wait my dears.. We have only just begun to see the potential of this tiny thing. It has the power to sweep over the entire planet to create the beautiful world we all desire" said Xerosic who was older, almost in his middle age, with red spiked hair, plump body and oily voice, he was clearly the team leader.

The holo caster flashed near Xerosic. He pushed a button.

"Z1 has escaped again through our clutches.. But it was all Celosia's fault. She let a bunch of kids get away with it" reported Mabel, blue haired team flare scientist through gritted teeth.

"You were the one who lost to the girl of that group. I was battling those two annoying boys all by myself.!" Purple haired Celosia defended.

"Don't fight. Don't fight my dears. Recover z1 this time. Celosia, Mabel, call the hq if you require assistance." Xerosic said in his usual oily voice.

"Oh yeah. Call me if you can't handle this. I can recover z1 in a minute you know" it was Aliana's turn to gloat at rival's failure.

"I don't need any help from YOU. I can recover z1 by myself!"

Xerosic ended the call before the rivalry could get ugly. He turned to the captured Zygarde core.

"See my friend. The core is emitting energy far beyond than what we predicted. We have a duty to put it to 'good' use" he snickered.

 **Pokemon center**

After fending off attack on squishy the day before, our heroes were enjoying breakfast at a pokemon center.

"Man oh man! Why can't Kalos league begin sooner?.. Pikachu and I are so fired up, we can't wait that long"

"Pika-chu"

"Now now Ash" the former gym leader tried to talk sense into Ash.

"Not everyone is as quick as you or Sawyer to collect all badges and weren't you going to use this time to train?"

It worked.

"Right. training.. We'll use this time to pump up our attacks pikachu"

"pika pika-chu" the little rodent's tone matched his trainer's excitement.

"But where can we do it?"

"There's mt. Aquamist behind the pokemon center. How about that?"

"Sounds good to me alright. Ready Pikachu?"

"Pi ka"

"Serena why are you smiling?" Little Bonnie was more perceptive than the two boys.

"Um oh nothing at all..." Serena shook both her hands in front of her to assert her point" "um I was thinking it's been a while since I trained with my pokemon too"

She blushed.

 _Why'd she blush at that,_ wondered Ash. But it was not in his nature to think too much.

"Then you can train with me and Clemont, right Clemont?"

"Of course, a battle is all you need to feel better Serena."

Bonnie thought both Clemont and Ash were soo dense but she followed them to field at the foot of the mountain.

 **Ash vs Serena**

"Braixen flamethrower"

"Noivern supersonic"

The two moves collided but Braixon ended up confused as a result of supersonic.

"Snap out of it Braixen, use sunny day then flamethrower"

Sun shined brighter above them, in the next second a massive fire erupted from Braixen's wand aimed at Noivern but the dragon pokemon was quick to dodge.

"Boomburst"

Noivern's ears flashed silver, releasing damaging sound waves. Braixen couldn't take it..

Braixen is unable to continue. Noivern is the winner. Clemont declared. "Good job though Serena. Now it's you and me Ash"

Someone was attracted by the flame and the noises on mt. Aquamist.

"Finally, we've located z1" blue haired Mabel's high pitched voice squeaked in microphone.

"Proceeding with z1 recovery" said her purple haired colleague Celosia.

"Hold it Mabel, Celosia. Standby until tomorrow afternoon. A very special person can join you then" Xerosic commanded.

"We can handle the kids."

"It's Lysandre's orders"

Mable was too smart to argue.

"Roger"

 **Back at the center again**

"Wow that was some rigorous training, I'm hungry. What about you buddy?"

"Pikachu" pikachu agreed. They were back in pokemon center, all tired. Clemont and Ash had full battle where Ash very narrowly beat Clemont. Serena and Braixon attempted to learn a new move called mystical fire. Sylveon learned dig and was working on protect. She was failing to keep the barrier up under physical attacks. After the master class was over, Kalos queen Aria had told the runner up contestant Serena to make her pokemon strong as well as pretty. Therefore Serena was doing what she never did before, battling and making her three pokemon stronger. It was already Paying off. Flames shot from Braixen's wand burned bright and sparkly. Sylveon was showing great confidence in herself. Her newest addition, ralts whom she captured using Sylveon, had evolved into Kirlia. Serena herself was getting even better at coming up with creative combinations. She was sure she and her pokemon could be of help in battles as well as in trouble with team rocket.

They all were happy with their efforts and satisfied with their pokemon's.

After they got their pokemon back from nurse Joy, decided to call it early night.

Little did they know what plans Celosia and Mabel were making for them that night.


	2. Protecting squishy :O

**A/N More chapters on the way! Team Flare strikes and battles begins right in the pokemon center.**

* * *

At midnight,a team flare grunt entered pokemon center through an open backdoor. He made his way to the large guest house for traveling trainers, he looked at the picture he held. A little blond girl with yellow bag laughing with other three children. The eldest was her brother, he was told. His job was to catch a certain green pokemon from the little girl's bag. He wasn't told anything more.

Squishy couldn't sleep. He looked at his friends Bonnie and Dedene, they were both asleep. All familiar, kind faces were asleep. He felt uneasy and hid deep inside Bonnie's bag, his little safehouse.

Grunt opened various rooms on ground floor. _A trainer with Froakie, wrong room. Two dark girls with red and blue bags, wrong room_ He thought to himself _. Four children with a little girl, correct room.. Finally_. He broke in stealthily. His orders were to retrieve the green core drawing as little attention as possible.

He checked the room, trying to find it. "Squishy, that you?" Bonnie mumbled.

"Squishy?" She tried to feel him.

"What's wrong little sis?" Clemont was groggy. He put on his glasses and turned on the light.

"Hey who're you!" He yelled. Taking out Luxray's pokeball.

"Looks like we have to do this the noisy way" Celosia coldly said to Mabel. They were supervising the situation from a distance. "Drapion, come on out"

Mabel was already moving into pokemon center where a fight was over between luxray and a Houndoom. Houndoom was knocked out in one hit and grunt had jumped out the window.

Celosia took his place in the pokemon center's window when Drapion blocked the front door of the room.

"Give us z1 now" she smiled at the cornered, sleepy kids.

"You're team flare. What do you want with squishy?" Serena exclaimed, her temper rising.

"Oh haha.. We've hardly got time to chat blondie... You!" Celosia stopped smiling and glared at Bonnie "where have you hidden z1?"

"No way I'm telling you! What do you want with it?" Shouted Bonnie.

"All right then. Drapion pin missile"

"Pikachu, Luxray thunder"

Drapion was paralyzed. "Run" yelled clemont.

They picked up their bags and pokemon and ran out.

"Oh my. What's going on here?" Nurse joy was on her way to investigate noise.

"Team flare. Quick nurse joy, where can we hide?"

" follow me"

"I have called officer Jenny " Nurse Joy told them seriously.

They had changed into their day clothes and awaiting officer Jenny.

Squishy was safe and hidden inside Bonnie's bag.

When officer Jenny arrived, there was no sign of team flare. Jennny was furious with them for damaging public property.

"All right kids, you better tell me everything or spend the night in Jail" she stared down them with her blue eyes with her hands on hips.

"They are called team flare and they were after.. s.. pokemon"

Clemont decided not to tell her about squishy. Walking around with unknown being with mystical power was sure to arouse suspicion in a cop.

Bonnie looked at Clemont but Serena looked at her with no-talking-now expression.

She looked down and kept quiet until Jenny left.


	3. Alain appears: where is squishy?

**A/N This chapter is pretty intense. Alain shows up with his mega Charizard and Ash and Serena have to fight side by side with Clemont. I have tried to describe battles to the best of my ability! Enjoy !**

* * *

After the surprise battle with Celosia and Mabel of Team Flare, our heroes are in pokemon center.

"What do we do? We can't stay here forever." Serena was worried.

"There's a Casadina city ahead. It's a huge place. Security cameras everywhere and electronic surveillance system of pokemon center is the best in all Kalos." Clemont rambled on about the equipments. It was well known that he loved technologies.

"Then let's go there." Ash agreed. Eager to keep squishy safe from team flare and resume his special training.

As they were nearing Casadina city, they saw helicopters.

"Oh no. Not them again." Bonnie cried.

" we got you cornered now. No nurse Joy or officer Jenny here to disrupt our mission" said a cold voice with a hint of smile. Of course that voice belonged to.. you guessed it! The Team Flare scientists.

"Drapion pin missile"

"Houndoom dark pulse"

They attacked without warning. Purple and black waves flew at them along with silver vines of pin missile.. Luckily Clemont had good reflexes with experience of dealing with crooks as a gym leader.

"Luxray thunder" Crackling bolts of yellow electricity collided with the dark pulse and pin missile, keeping their enemy from advancing.

"Noivern boomburst" Ash joined. The sound based move didn't hurt Mabel and Celosia who were wearing headphones but pokemon were shaken.

Of course they didn't care.

"Drapion cross poison"

Luxray and noivern had to dodge.

"Aim cross poison at the girls"

Drapion turned to Bonnie and Serena who were hidden behind a rock, away from the boys.

"Sylveon protect" yelled Serena, throwing pokeball in the air. Sylveon struggled to shield them inside green barrier.

 _I better do something fast_ , Serena thought, her sense of urgency increasing. _Ash and Clemont are outnumbered by grunts and Sylveon can't hold protect barrier for long yet_.

"Braixen mystical fire" she screamed.

Roaring fire in shape of rings burned drapion, decreasing his sp. attack. He recoiled from the heat.

That was enough. "Sylveon use fairy wind". Sylveon pulled herself together, whipping up a silver tornade aimed at Drapion.

Drapion seemed to be suffering from an effective attack but Serena knew they had no chance of winning when they were outnumbered 10 to 1 and their adversary had technology to capture squishy by force.

"Bonnie come with me"

"But Clemont.."

"Now!"

"Charizard block them"

Massive charizard stood in their way, ready to strike at his trainer's command. They didn't want to fight him. Serena tried to go around it, pulling nervous Bonnie by her arm.

Mabel and Celosia stood on both sides of Alain and charizard now.

"Keep the boys occupied. We'll do the recovery operation" barked Mabel in mouthpiece.

Serena stood in front of Bonnie with her arms wide. Shielding her, dedene and squishy from team flare.

"Braixen mystical fire, Sylveon, fairy wind"

Charizard wasn't hurt by the fire. Alain decided to take Sylveon out first.

"Charizard use shadow claw"

Charizard's claw turned blushish and long, nails sharp. Sylveon dodged and used disarming voice. A soothing voice filled the field, making Charizard so tranquil that he wouldn't fight. In that moment, Braixen used psychic.

Silver glow surrounded Charizard, rendering him unable to control his limbs and in another second, he was thrown in the trees behind him by Braixen's psychic.

Alain only seemed amused.

"Charizard, show them the strength of our bond. Go beyond evolution! Mega evolve" Alain pressed the bracelet and the mega stone and key stone made contact.

A charizard was bad enough as a foe but a mega charizard was even bigger problem.

"Clemont, help" Bonnie was shouting but he was fighting alone, surrounded by grunt's houndooms from all sides, all attacking at once.

"Serena, what will you do?"

Serena thought of Ash and what he would do. There was only one thing to do. _I WILL NOT GIVE UP_ she Thought as she stood with her head held high, facing mega charizard directly with her two partners.

Celosia took a step closer.

"Sylveon, keep them away with fairy wind"

She was thrown off her feet as fairy wind blew full force. Celosia decided to leave it to Alain.

"Dragon claw"

"Disarming voice, braixen use psychic"

Charizard was thrown off again but it wasn't as effective as the last time. He simply brushed himself off, resumed the attack and aimed it at braixen. Dragon moves won't affect sylveon.

Braixen was thrown off, she hit the rock hard.

"Braixen" serena cried. She took out her third pokemon, a Kirlia.

"Hold them off till I check on braixen" she shouted at them, running towards Braixen who was buried under small rocks.

Kirlia used charm, Sylveon disarming voice to buy time.

Serena and Bonnie threw away some of the rocks, underneath a fire was burning.

"Is that you Braixen? I will get you out.. Hang in there" she got to work.

Fire burned stronger, next a huge rock on the fire moved on its own and launched itself at mega charizard, who was attempting to use shadow claw on kirlia.

"Braixen.." Serena was astonished. "You evolved"

"Del-phox" _Thank god_..

"Alright then, kirlia use charm, delphox, mystical fire"

Kirlia looked charmingly at Charizard, making him wary, in that moment a yellow and red ring of fire, larger than any of them had ever seen before hit him directly on chest.

But even with the hits, Alain's mega charizard was equal to the three of them.

He used blast burn then steel wing against the two fairy types, knocking them unconscious.

"Delphox use psychic again, Bonnie, you need to run with squishy now. I can't protect you."

"But.. Where?"

"Just go.. We'll find you"

"Thank you Serena"

She didn't look back.

She had to buy them as much time as possible. Celosia and Mabel tried to go after Bonnie. Delphox used phychic on them, tossing them in the air.

This however was when their luck ran out.

Mega Charizard landed blast burn on delphox, then hid behind the fire and launched dragon claw, aiming at Delphox.

Just then, Ash and Clemont finished taking care of grunts and joined Serena.

However all their pokemon were tired.

On the other hand, the two girl scientists had sour heads from being tossed but they could walk. They went after squishy without wasting any time.

"Don't hurt Bonnie" was all Clemont said before passing out himself.

"That was never our intention" said Alain as called his victorious mega charizard back.


	4. Emotional wrech :(

**A/N Hey there! This chapter contains some emotional Ash-Serena moments and Clemont-Bonnie moments. I wanted to include some emotions because the next chapter is all about Team Flare's evil plans with the Kalos legendary trio. I wanted to do Alain's back story but I couldn't come up with anything that fit with Zygarde arc.**

* * *

They all woke up inside a hospital next to the Casadina pokemon center. Ash was the first.

"Pikachu?" He said expecting a reply. There wasn't one.

He called again, still half asleep.

He woke up suddenly, realizing Pikachu was gone.

"Easy there young boy. Nurse Joy is looking after your pikachu. You can go see him after I give my permission" Ash looked at the man who spoke.

He was still groggy. The man wore glasses and a white coat. He was in a hospital.

He looked at the unfamiliar surroundings, the events of.. wait when was it exactly.. Came to his mind. _Team Flare had attacked them.. They wanted... Something.. Squishy! Where were Bonnie, Clemont and.. and Serena?_ Fear clouded his mind.

Doctor seemed to understand his worry.

"Your three friends are still asleep. They are not hurt, just tired. Step in my office for paperwork please. I have to let officer Jenny know you're awake."

 _So they were okay.. Not as bad as he feared at least._

Something clicked in Ash's mind.

"Where are our bags?"

"In the locker, they were found lying right next to you when our ambulance picked you up. please collect it when you leave." The doctor was getting annoyed with Ash's slowness.

"Do you wish to remain here a little longer? You don't seem very fit to me"

That did it.

Ash snapped out of his shock.

"No. I'm fine. Please tell me what I have to do to get our bags right away"

 _It_ _was essential to make sure squishy was there and it was safe._

If the doctor thought it weird, he didn't show it.

After Ash collected and checked their belongings, he ran headfirst into Serena. Oops!

She was too tired to blush but she was happy Ash was okay. That happiness didn't last when Ash told her squishy was missing.

"Oh no.. Poor squishy" tears flowed from her eyes.

Ash regretted his lack of tact in telling bad news.

"Serena, no.. Don't cry. I'm going to get squishy back no matter what"

"But Ash what about it's safety? What if squishy gets hurt?"

Ash had no instant ideas.

"Let's find Clemont and Bonnie." He attempted to divert her attention. She wiped her tears.

"Umm.. Maybe you let me tell them about squishy Ash?" That came out as a question. She didn't want to offend Ash but she wanted to do it as gently as possible. Bonnie would not stop at couple tears, she will wail, cry and worry aloud. Such response won't be helpful to the three of them to come up with a course of action.

They found the room.

"Hey Clemont, how do you feel?" Serena asked softly.

"Why thank you Serena. I don't feel good but I m glad to see you and Ash safe."

Bonnie was asleep. Now was a good time to tell him.

"Um.. Have you seen squishy after..umm We ran into team flare?"

"No. Wait..You don't think..."

They all looked at Bonnie at once.

"Let's keep it to ourselves for now. Squishy may not be in her bag but he might be in pokemon center"

They had hope again as they woke Bonnie and went to pokemon center. Luckily she was too tired to ask questions.

Their pokemon had recovered completely. They had a happy reunion. Each trainer was proud of their pokemons for standing up to Team Flare.

It ended quickly when Bonnie asked about squishy. All pokemon looked at them wondering the same thing. Their silence seemed to speak volumes. Of course Bonnie didn't understand it. She clung to Clemont repeating her question louder and louder.

"We don't know" he told her. she started wailing loudly. The incident was too much the child.

"But I promise you Bonnie, I will do my best in finding squishy and rescue it"

"Me too" joined Ash.

"And me" Serena.

"So what we need now is information"

"Leave it all to me. The future is all upto science! Ladies and gentlemen, what I present before you is the supercomputer with programs, which I developed myself. It can hack into any file of any system with the correct keywords... Let's see. First keyword is Team flare"

Many files were found. Clemont encouraged Bonnie to look after all the pokemon. Of course they didn't really need looking after but he wanted to keep her occupied. Serena's Kirlia amused her by teleporting from one side of her to other.

They returned to the enormous files. They knew nothing except the organization was called team flare. They couldn't find who ruled it or how many members existed or anything..

They still kept at it, barely taking a break when Ash decided to take a walk around the pokemon center.

 **Sawyer**

" Ash hello" someone called.

"Hey Sawyer" Ash said to the green haired youth.

The last Ash and Sawyer met was their battle before Ash challenged his eighth gym. Sawyer had beaten him. He had gotten all his badges before Ash. On top of it, he beat Ash in a three on three battle. The battle had left them amazed. Sawyer's pokemon's strength was remarkable. They seemed to have leveled up very quickly and thoroughly. Sawyer seemed much better in terms on moveset and strategy himself. Clemont and Ash had attributed his quick growth to studiousness. He always carried a little notepad with him to take down whatever new strategy he heard in conversations.

"What have you been upto since the last time we saw each other?"

"Oh I battled Wulfric and got the iceberg badge" Ash told him.

" I knew it! I had completed faith that my senior won't let me down."

"Ah well thanks!" Ash laughed childishly, embarrassed by the compliment.

" So did you see Team Flare again?" It was so sudden that Ash jumped. _How did he know?_

"Why do you ask?" He wanted to know.

"Um well since the last time, I had a run in with them in this area myself"

"Where did you see them?" Ash wasn't going to let up.

"I don't exactly know where.. I was lost in the dense forest behind mt Aquamist and I heard them move."

"Come with me. we have something to tell you." Ash led him to where Clemont and Serena were sitting.

 **The clue about Alain**

"What! they kidnapped squishy? That poor thing!" Sawyer was shocked. He was always curious about squishy. He had made a sketch and a point of showing the sketch around to pokemon experts if he met them. He was taking it to various gyms he challenged or to a knowledgeable nurse Joy. Nobody could tell him what squishy was.

"Wasn't Alain the trainer who wanted to battle greninja? I remember it clearly even though it was a long time ago. I had lost to Ash already and a passerby challenged him to a battle." Sawyer told them.

"Of Course! How could we not recognize him! He had a charizard AND he had a megastone and a key stone. Alain is with Team Flare!" Ash's brain finally started working.

Clemont immediately put Team flare, Alain as keyword into his computer program and it started searching files matching those key words.

Serena was surprised. "I can't believe that sincere looking passerby was our deadly foe yesterday. Yet he looks so different. He is nothing like the grunts. I can't believe it. " though she spoke she knew in her heart that this was no mistake. They had seen Alain and his charizard both times. It was definitely him.

Clemont recovered first. "don't assume things without sufficient data."

"WHY NOT?! how can Alain be innocent Clemont? If you don't remember, I do. I WAS THE ONE BATTLING HIM! HE ALMOST BURIED MY BRAIXEN WITH THAT MEGA CHARIZARD OF HIS!" Serena's temper rose with the memory.

"I'm saying nothing of that sort. Cleary Alain is with Team Flare and definitely involved into their evil operations. And YOU were the one who said he was sincere!" Clemont shouted back.

"SO WHAT ABOUT MY SQUISHY?" Bonnie yelled.

" WILL YOU STOP FIGHTING!" I can't think because of you guys" Ash shouted at them.

" oh really! YOU and THINK Do you even UNDERSTAND how to do it!" Serena screamed.

Pikachu and Dedene were close together, annoyed by their trainers when Dedene's cheecks nuzzed against Pikachu's body. Pikachu freaked out.. And

"Pika-chuuuuu" a massive thunderbolt hit everyone in the room.

"WHY ME?" Sawyer lost his temper.

"PIKA!PIIKACHU PIKAPI PIKA PIKA CHU" Nobody understood the language but from the way Pikachu jumped in and shouted at them all, they got the msg "stop fighting"

They realized they weren't getting anywhere with fighting. Squishy's abduction and Alain's actions was not their fault.

Clemont quickly checked the new data on Alain. He couldn't find any criminal history against him before he joined team Flare. He actually was professor Sycamore's assistant and he quit because he wanted to beat all mega evolutions with his mega charizard. Clemont's program couldn't hack into Team Flare's computers or they would have access to his current whereabouts."

"Shall we talk to professor Sycamore then? He might be able to give us something to go on."

* * *

 **A/N I'm having Team Flare boss Lysandre appear in the next chapter. I have also thought a bit about how Lysandre is as a person and used it in my story.**


	5. Power of the trio: Flare's ambitions

**A/N Contains Anime reference. For those of you who don't know, Olympia, the Psychic gym leader made a prophecy that Kalos will have a crisis and Ash and his friends would be involved in it.**

* * *

 **At Professor Sycamore's lab**

"Alain! no way! You must be mistaken. He is a kind, hard working nice fellow. What's he got to do with Kidnappings? He can't gain anything by it" the professor was astonished by what he heard!

"Oh we don't think squishy was taken for personal gain professor."

"What is it you suspect?" said the respectable professor. He was getting worried now. If his former employee was using the knowledge he gained at Sycamore lab for evil, he would feel betrayed. Not to mention loss of public opinion, or worse, being suspected as accomplice.

"Something bad no doubt!" Bonnie was pessimistic.

"Professor, what can you tell us about Zygarde? We heard Team Flare mention it in Terminus cave" Ash racked his brain, impatient to track down whereabouts of squishy.

"Well..we don't know much about Zygarde's exact powers but he, along with Xerneas and Yveltal is responsible for balance between pokemon. but I do tell you this young Ash, powers of Zygarde exceeds those of Xerneas and yveltal and if an evil organization has them, it means bad news for Kalos"

Olympia's prophecy shot in Ash's mind. Could she have foreseen this? but something was still missing.

 _What was squishy? Why was Team Flare after it if it was supposed to be after a huge pokemon like Zygarde?_ Clemont wondered.

"Do you know where Alain is Professor?" Serena was desperate for any information for Bonnie's sake. The poor kid has too much to deal with.

"I'm afraid I do not know Serena. I wish I could be of more help. but I promise to do everything in my power for squishy."

"Thank you professor."

That wasn't particularly helpful. Their doubts had simply been confirmed. They had to track down Squishy's location and get it out safely with even more urgency and they still had no clue where it was.

 **Lysandre's lab**

In a rectangular room behind Lysandre cafe, cages of Squishy and z2 were placed on tables facing each other, separated only by a large tray between them. They were connected by a small beam of light.

"Confirm link between the two cores"

"Confirmed"

"Expose the link field to water"

"Check"

Water flowed in the tray between squishy and z2 and rose a little.

"Put the meteors in"

"Check"

"Simulate cores"

"Simulating"

A beam prodded both cores into irritation. They emitted light to throw it off. The flash was dazzling. Everyone closed their eyes..

Inside water, turquoise stones were shining softly.

"Are we successful?"

"Bring eevee"

"Contact stone with eevee"

It turned into Vaporeon..

"Water stone confirmed"

"Oh haha... Our generations knew evolutionary stones come from meteors but we are the first ones to make one ourselves. I have proved that my theory was correct. Zygarde is capable of many great things. One of which is forming evolutionary stones. When meteor is exposed to Zygarde under water, it becomes water stone. If we expose it to fire, it would become fire stone... Oh haha.. We can now control pokemon evolution itself!... Oh dear, please tell our boss the experiment is successful. He will like it very much."

 _This is nothing.. Just wait till you see what else Zygarde has to offer boss.._.. He kept that thought to himself. _Now was not the right time.._

 **Lysandre**

In an elegant office, A tall man resembling Pyroar was sitting in a comfortable recliner staring out the window peacefully. A red haired man with oily voice was chattering away in mirth.

"Oh ho ho..Just as I predicted. We have confirmed that the cores react when they come into contact with the ancient meteror, that energy has qualities to become either a mega stone or key stone. But which one it becomes will depend on whether the meteor is exposed to the aura of Xerneas or Yveltal. If the meteor was exposed to Xerneas's aura, it becomes a mega stone.

As we know, megastones are of numerous kinds. Garchompite for Garchomp, Gardevoirite for Gardevoire etc... You see sir, Xerneas aura is quite versatile. It can sense all the pokemon in our ecosystem and transforms meteor to take form of various mega stones as per their need.

Yveltal aura is unchanging. When meteor is exposed to him, it can only turn into keystone."

"So Xerneas can balance the number of mega stones for each kind of pokiemon?" Lyssandre spoke as if to himself.

"That's correct sir"

"Is that all Zygarde is capable of Xerosic?" _Are you sure you're not keeping anything from me?_

"That is all we can confirm right now sir" He placed emphasis on _confirm_ and continued

" Zygarde's potential is magnificent. We have several other hypothesis which Mable and Celosia are preparing to test. I have Bryony and Aliana running experiments as we speak."

"I see." _Never mind. Don't trouble me with unproven theories_.

"I'm happy we have solved the mystery of evolutionary stones Xerosic. How perfectly nature has ways to maintain balance between pokemon. Yet it is so crude. There may be mega stones for every pokemon on this planet. But they might be hidden away in quicksands, caves and other unreachable places. Such a waste.. Such a waste.. HOWEVER, I SHALL MAKE IT RIGHT! I shall make the world beautiful again.. I shall control everything. Pokemon, their evolutions, mega evolutions and powers! Xerosic, find out how to artificially make mega stones of pokemon of our selection. We shall take over Xerneas's power. WE shall determine what mega stone to create, how many and when! Then we will use Yveltal to get matching key ... Pretty soon the power of mega evolution will be in my grasp"

The scientist did not find it strange that Lysandre stared out the window the whole time he addressed Xerosic. Some people might have considered it rude but everyone who worked for him must be used to it.

The scientist took leave.

The man faced himself in a wall size mirror in his office when he was alone, _I now have a complete monopoly over artificial evolutionary stone. Pretty soon I shall have the entire mega evolution under my control.. Then destroy all the current stones and I shall control evolutions of the entire world_ "Oh HAHAHA" Lysandre laughed aloud and sinisterly, unable to contain excitement. He never laughed in front of people somehow.

His face then turned serious and his body tensed.

 _Yet, The power of Zygarde is only beginning to show itself. Such potential was overlooked by our foolish ancestors. I shall make it right. The world will soon be much better_. He kept staring evenly at his lionlike reflection.


	6. Immortality, Life cells & Absorb cells

**A/N Thank you for so many views :) ... I have updated the previous chapter to better connect with this one. This is the big chapter about Zygarde's true potential, his relation with Xerneas & Yveltal and the real ambition of team flare! Enjoy :)**

* * *

 **Lysandre's office**

Xerosic's short quick steps were heard in the spacious circular office. The man himself appeared, nervous and fidgeting with a red jacket he wore.

"what is it? More news about Zygarde?

"Yes my dear sir.." He said in his usual sycophantic manner. _I must do it… for sake of knowledge and my fabulous research._ He worked up the courage and blurted out, "our research has come farther than any man has ever seen. We have reasons to believe there is far more potential to Zygarde that asks to be utilized. Therefore I'm here to reques ah more funds for the mission"

 _Hmm… more than I provided?_ The Team Flare boss wondered as he continued staring out the window from his recliner, which was faced away from Xerosic as usual.

"How much?"

"another 30 billion"

 _Surely you don't think I will just hand it to you_.. He said in his usual assured manner, "I'm committed to gain as much knowledge as I can about mysteries of pokemon in my own way.. no amount is too big to unravel the mysteries of the universe. How does your research fulfil my goals Xerosic?"

"Well sir. My assistants Bryony and Aliana have found multiple Zygarde cells in Xerneas and Yveltal's bodies. There are two types of cells X & Y. The red colored X cells give the ability to give life while the power to absorb life comes with Blue colored Y cells. Together Xerneas and Yveltal maintain the balance of the universe by creation and destruction of various kinds of lives. We believe Xerneas and Yveltal both came from Zygarde, Xerneas from the Red colored X cell, Yveltal from the blue cell Y… and that is why Zygarde is more powerful than the two of them, because it created them"

"So Zygarde cells, depending on type can both give and take away life on the planet?"

"That is what we need to confirm sir. This experiment will not be easy. Tremendous technology, best of manpower & supplies shall be used." He paused for dramatic effect. " No stone shall be left unturned for human to be able to possess the ultimate power of the nature."

With Lysandre's back to him, Xerosic could not see his boss's face to see what effect his speech had on him. He decided to make his case stronger.. Luckily he had saved the best for the last..

But Lysandre could see him very clearly in the window glass, more closely than it was believable… He could see from the way he opened his mouth to speak and closed it, that he had something more to say…

"Also sir, Bryony and Aliana's research shows that Zygarde cells do not perish.. That's what gives eternal life to Xerneas and Yveltal.. If we found a way to put those cells in a human body…." Xerosic didn't need to complete the sentence. _That human would have the power to destroy and recreate the entire universe AND be IMMORTAL._

The recliner's quick turn surprised Xerosic… he started fidgeting with his red jacket again as Lysandre's lion like face turned towards him directly with curious expression.

"This is excellent indeed. The funds shall be arranged."

"That is very generous sir.." Xerosic relaxed and he felt excitement as he nodded sycophantically at his boss...

"You can go to the lab. I shall ensure a way to finance this operation"

 **POKEMON CENTER**

" _And now Poke news has the most special report that THE WELL KNOWN LYSANDRE LAB has come up with a way to ARTIFICIALLY develop THE POKEMON EVOLUTIONARY STONES, MEGA STONES AND KEY STONES (pause) that's right our dear viewers. The elusive mystery of pokemon evolution is on its verge of being solved. The stones will be available to SALE at your nearest poke mart. According to Lysandre lab spokesperson, Evolutionary stones and key stones will be available for immediate sale whole pokemon specific mega stones are special order only…_ "

An excited chattering crowd of pokemon trainers gathered around the Tv in the Pokemon center, Ash, Clemont, Serena and Bonnie included.

"hmmm.." Clemont started to say something.. _My supercomputer showed that Team Flare had been working on mega evolution, that man Alain was into mega evolutions.. wonder if there's connection_..

The phone rang by his side.. the string of thought was broken.. _Professor Sycamore calling_..

"Hello Professor" Clemont answered the video call.. Bonnie ran to get Ash and Serena who were excitingly discussing the news among the crowd.

"Hello kids.. I see you are aware of the news already" Sycamore added looking at the TV in their background.

"It's unbelievable. I can't wait to go to the poke mart, right Pikachu?" Ash was impatient as usual while Pikachu was uncharacteristically quiet. _Could the little yellow pokemon be feeling as if something was not quite right?_

"Not so fast if you please." Sycamore cautioned "Now listen here very carefully. After you visited me in my lab the last time and told me about squishy's kidnapping and your suspicions about team flare, I alerted the Kalos Anti Crime Unit at once." He paused to look at their serious expression and blurted, "I cannot give any more details over the phone. Meet me in my lab as soon as you can. You will find everything you need."

They all looked at one another wondering what the last sentence meant.. " _You will find everything you need_ ". There was little time to ponder upon it. The professor had something important for them and they had to be in Sycamore lab as soon as possible.

Clemont used internet to book four tickets to Lumiose city where the lab was located.

 **Three months later at Lysandre Lab**

The lion like Lysandre sat patiently in the conference hall as the plump red haired scientist Xerosic boasted how his experiments confirmed that Zygarde cells indeed did have the power to give and absorb life. The red cell X, which his assistant Bryony found inside Xerneas gave life while the blue cell Y in Yveltal, which Aliana was credited for absorbed life from the planet.

Both life cells and the absorb cells were produced from the energy from Zygarde's transformation, when it transformed into 100% form. The energy from 10 or 50% forms was simply not sufficient to form the cells.

The presentation went on. Lysandre's expression was giddy as he heard it, his body leaned towards to speaking scientist unconsciously, indicating he was listening very intently.

 _Finally.. I shall be able to ENSURE world peace._ Lysandre was thinking as he listened to the boasting scientist. _With Zygarde cells in my body, I shall be able to both CREATE and ABSORB life of an entire town or even region.. If any government didn't comply with me, I shall have powers absorb life from their region… on the opposite if any region pleased me, I could give a boost of life to their flora and fauna as well as minerals and resources… How peaceful the world will be.. with no power to fight as I shall possess the ULTIATE POWER.. Nothing can break my perfect system for I SHALL BE IMMORTAL!_

"You have done very well my Team. Now you must put both the cells in my body" Lysandre stared at his employees over conference table.

"Certainly sir. Our surgeons are more than upto the task. But first you must make Zygarde give you the cells sir." Xerosic said in his usual oily voice.

In the surgery room, Lysandre addressed the two cores, squishy and z2. "I, the boss of Team Flare, supporter of the peace stand before you. I order you to submit yourself to my command and bestow upon me, the life cells X and the absorb cells Y."

"Never, human. I do not bestow my power to the unworthy." The cores said unanimously through telepathy.

"HOW DARE YOU? I have uncovered your powers and it is only right that I get to unleash it", he roared, his face contorted at being called _unworthy._

"You brought us here forcefully, wish to capture me against my will and use my power to become the ruler of the universe. I shall not allow this." This was squishy.

"You have only proved that humans cannot be trusted." Z2 was adamant on his bias against humans and seeing how team flare had treated it, it had a good reason.

"Very well" Lysandre said smoothly. "You stand before me unreasonable and defiant. I have other ways to get those cells" He paused. Everyone was staring at him with rapt attention. "From the bodies of Xerneas and Yveltal." He continued looking down at the cores evenly. "You know they both enjoy eternal life only until they have your cells inside them. If I take them, they shall perish just like.. ah _any other_ pokemon." He smiled silkily in vindication.

"Kill Xerneas and Yveltal? That cannot be allowed!" The cells exclaimed in indignation.

"But I Lysandre, must possess life cells X and absorb cells Y to bring ideal world order, you silly pokemon. Your powers are no longer legendary. They shall be known and possessed by me, a human, at the cost of the two pokemon whom YOU let die as a price of your defiance".

Everything happened suddenly after that.. green cells started surrounding squishy and z2, their size increasing..

"HAHAHA... The energy from Zygarde's 100% form will give me the ultimate power to command the universe" Lysandre thought he won... However…

 _Oh no! thought Mabel who recognized the symptoms and she knew exactly how dangerous Zygarde can be when transformed from first hand experience, although they had encountered only 50% form._ Aliana seemed to be thinking along the same lines. Unfortunately for them, their laser guns were exactly where they were supposed to be, inside the lab. They only had their pokemon on them when they accompanied their leader to surgery room. Their leader had made the mistake of assuming Zygarde will give in to his demands to protect the other two legendaries.

Zygarde's cores were speedily gathering light; the sinister green glow of cells grew larger and larger until it became a huge green and black serpent with five heads and its body in shape of Z.

"You seek to threaten the life of our whole planet human! You shall not succeed!" Zygarde 50% form's telepathic voice was magnified.

"Subdue it Team" Lysandre ordered… Nobody had brought their sophisticated weaponry in the surgery room. They all took out their pokemon.

Meanwhile the team flare boss took this chance to escape while the chaos ensued. He ran into an open field nearby, made a phone call and spoke a few urgent words to someone.

* * *

 **A/N By the way, I got the color idea for cells from squishy and z2's colors in the anime. Squishy's core is red while z2's is blue :) :)**


	7. Preparing to save Kalos

**A/N Hi again! Thanks for the awesome views and reviews :)**

 **Hi. I have divided my previous 3000 word chapter into two parts and this is part one. So in this chapter, everyone learns the truth about whats going on. Ash and team learn the truth of team flare/Lysandre lab. In the next part, we learn the truth about why Alain was working for team flare. The BIG twist is when Zygarde... lol I'm not giving THAT away. You will have to read the chapter... Enjoy :)**

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 **Three months before in Sycamore Lab**

"Wow this is really amazing!" "pikaa" Ash was amazed as he stepped into first floor of professor Sycamore's lab. Bonnie ran straight inside, ahead of all of them. The others explored the place. The offices where new trainer's pokemon were kept, the assistant's rooms were all located downstairs and the first floor room was converted into a monitoring unit. Occupying the wide room, where officers from Kalos Anti Crime Unit had been camping temporarily, were dozens of computers, some showing footages from different areas, some with maps and charts.

"This is really…. _advanced_ ", Clemont's eyes were sparkling with excitement.

"Squishy is not here" Bonnie greeted them tearfully before they had a chance to admire the monitoring unit further. She had entertained a childish hope that professor Sycamore had already found the Zygarde core and was keeping it as a surprise for her. The others knew better.

Before anyone else could think of something to say, Ash looked at the screens. None of them showed their little green friend. "No." He said flatly. "Maybe they haven't found it yet".

"I want squishy! Who knows what those bad guys are doing to it? He could be hungry or lonely or crying for me!" Bonnie had entertained too big a hope to bear it having been false. She sat down and continued sobbing while Clemont started reassuring her that they will find squishy definitely. Bonnie was soothed a little. She was still sobbing, but at least she wiped down tears from her cheecks.

Clemont had few more words of comfort to offer but now he really wanted to know about what Sycamore had discoved. He looked at Serena for help.

"Bonnie can you help me brush Sylveon's fur?" She took the clue and led Bonnie away tactfully.

"What was that all about?" Clemont inquired after the girls left. "Do you know something?"

"I once had a similar experience." Ash said curtly. "When the legendary trio of Sinnoh,

Uxie, Mesprit and Azelf were captured by pokemon hunter J, they communicated to use via telepathy, but enough about that. Let's focus on getting Squishy out safely"... he collected himself and shook off the disturbing memory.

"We have an intelligence that something is not quite right with Lysandre Lab" Sycamore told the boys when Serena walked back into the room alone.

"Sylveon is with Bonnie downstairs. I told them to stay there" She added quietly to Clemont, who nodded in response. The conversation continued.

"Why do you think Lysandre Lab is up to something?" Ash asked Sycamore.

"I'm referring to their recent marketing of mega stone, key stone and evolutionary stones. Something is fishy. I have been following the case very closely due to professional interest but I did not find any kind of information about how they were able to achieve artificially manufacturing the stones. Lysandre Lab has not shared any details about their own achievement. No interviews with the scientists, no papers published in journals, neither awards nor publicity. Their spokesperson refused to name the scientists behind it. I checked with other interested researchers and found the same thing. No one knew _anything_ about the manufacturing, where the lab was located or if we could visit the facility, NOTHING. No information at all." Sycamore was so engrossed with the mystery he seemed to have forgotten they were there.

"Why don't you let me use your computer professor? I bet I can hack and access _some_ files if not all" Clemont offered most confidently."Sorry" He added to an Anti Crime Unit officer who looked incredulous at the word _hack_.

"Actually that's not a bad idea at all. Give it a try Clemont." Sycamore checked with the officials. "Do you mind? Clemont is a Lumiose gym leader and he has excellent understanding of computers and programming."

It was okay. Clemont got to business. After eight hours, he appeared in the downstairs office where the others had been sleeping, panting and excited.

"I did it. Didn't get a lot of info but I think I know where it might be located. Come on"

"This is a possible location" He marked the digital map as he explained. "You see. it's in outskirts of Lumiose city… No one lives there. The land is mountainous and uneven. Read the name of the restaurant there…" His eyes gleamed. "Lysandre café"

The others seemed apprehensive. _Could be a coincidence…_

Ash spoke first "Let's check it out"

Serena was critical. "that's ALL you have after eight hours?"

Clemont scratched his head nervously.. "Umm actually… I couldn't hack into their files at all.. They' really well protected! I just googled Lysandre and this came up.." They all fell down anime style..

Professor recovered first. "Ah it's not much of a clue to go on but we should just have someone who could check it out, just in case"

"Wait! I know someone who does this professionally" Ash blurted. They all looked at him blankly.

"I will call him right away…"

Ash ran downstairs in office to use the phone.

"Hello Looker, it's me Ash. I need your help." He spoke quickly and quietly in the phone.

"Involved in bad business with some evil organization again Ash?" International Police officer Looker's tone was easy as he joked.

 **Three months later in Sycamore lab**

"I have confirmed it. After much hard work and concealment, I was able to check out the area around Lysandre café and they're indeed up to no good. I observed the people who hung around that place and clicked some photographs at great personal risk" Looker put pictures of Lysandre, Xerosic, Celosia, Aliana and some grunts on the table before them.

Ash, Serena and Clemont at exclaimed at the picture of purple haired Celosia… TEAM FLARE! In LYSANDRE LAB! They informed the officers quickly what they knew, all their previous encounters with the group! The police started running scans on their criminal database… _Finally! A breakthrough… They knew where to look…All thanks to Looker and Ash's brainwave in calling him at the right time!_

Looker continued with his findings. "I observed flashes of green lights in the area, along with occasional rainbows at odd times and a deep darkness all of sudden. Heard them mention z1 &z2 cells sometimes… Wouldn't know what those are, do you? And listen, I would act sooner than later if I were you, for I heard that they were going to move something to another secret location. Once they are gone, they may be so well concealed we may not even know where to find them again" His intelligent eyes twinkled at them.

"Zygarde" Ash mused. _In the Terminus cave when they tried to capture Zygarde, there was green light, when squishy transformed into doglike form (10%), there was green light…_

"Xerneas and Yveltal" there was no doubt in Professor Sycamore's tone. That was the only conclusion based on what Looker had said. _The rainbow might have been Xerneas's horns and aura, the dark aura should belong to Yveltal._

"It's team flare all right" Another Kalos Officer said, ready for the action. _I WAS told by Pokemon rangers that team flare captured the two legendaries and an arrest warrant has been out for their boss. Looks like we may be making some big arrests at Lysandre lab..._

Ash wasn't done. He was pep talking Greninja, Noivern, Hawalucha & Pikachu. His greninja had finally mastered Ash-Greninja form before Snowbelle gym match. They were going to walk right into the lab of team flare, arrest team flare's members, raid their assets and free the pokemon. Even though Ash had Kalos police with them, he was counting on his pokemon to stop team flare and save the legendary trio.


	8. Zygarde's wrath 1

Lysandre **Lab**

"Unworthy human, prepare for the end", in the little surgery room, fury of Zygarde's five headed serpent like 50% form knew no bound. Lysandre's plan of threatening and/or blackmailing the legendary had clearly not gone as expected.

The team flare members cried, pleaded mercy as they watched their pokemon knocked out in one hit and the room destroyed in the move called land's wrath. The roof had fallen down where Zygarde's head brushed… Their leader was nowhere to be seen. Debris had fallen everywhere and green flashes from the pokemn blinded their eyes.

The glow around the pokemon's body grew larger and larger. It became taller and leaner, more humanoid than anything else. Zygarde was in his 80% form and extremely angry with humankind that had wronged him, tried to kill his friends, captured him against will and threatened him. The ancient pokemon knew no distinction between good humans and bad humans. To it, humans of team flare represented whole humanity…

Meanwhile outside behind the bushes, Lysandre, while hiding himself STILL cherished the hope of Zygarde somehow transforming into 100% form and somehow obtaining the life cells and absorb cells from its energy which would make him immortal and in control of the planet. In his mad desire for superiority and power, he forgot all his reason.

Lysandre's attention was diverted as he noticed several helicopters over his head from where several people were getting down in the very little garden where he himself was concealed. _My back up is here at last_ … _Alain can take care of anything,_ Lysandre thought to himself.

Only it wasn't Alain, it wasn't even members of Team Flare. Ash followed by Professor Sycamore, Clemont, Serena, Bonnie and officials of Kalos Anti crime unit walked out, they jumped at the sudden burst of green light that came from nearby and ran to the source of it where the walls were now collapsing around Zygarde and fleeing team flare grunts.

"Squishyyyy.." Bonnie screamed as she ran inside the ruin of the room.

"Bonnie it's dangerous!" Clemont was panting from trying to keep up with the group when the sudden beam of powerful green light smacked them towards the broken tables.

"You will pay unworthy human for your greedy attempts for power" Zygarde's telepathic voice boomed at them.

"STOP! STOP ZYGARDE! WE'RE NOT YOUR ENEMY..WE'RE HERE TO HELP YOU" "PIIKA PIKACCHU" Ash ran forward and yelled, making Zygarde turn towards him.

"you are not trustworthy. Your kind has proven over and over that they're not trustworthy…" Zygarde's voice faltered towards the end. Squishy didn't support that statement. It trusted Ash, It trusted Bonnie, Serena and Clemont.

"NO! THOSE WHO HURT YOU WERE THE BAD GUYS AND THE POLICE HAVE CAPTURED THEM" Ash pleaded, refusing to back down when Zygarde advanced towards him.

"Nooo! You're all the same… Where were you when they attacked us with their weapons? Where were you when they captured my fellow pokemon Xerneas and Yveltal, the two who were responsible for maintaining everything around our universe? Where were you when team flare threatened to kill them for their own gain? You're NOT trustworthy and your kind shall be wiped out the surface of our planet to protect everyone else!"

Hundreds of beams of green light came out from its body aimed at all directions. They ducked and closed their eyes as they were thrown away with piles of debris. The trees and hills exploded and collapsed everywhere and rocks destroyed anything in their paths as they tumbled downwards.

"Squishy! Please stop this! I just want to be friends with you and play with you. We never hurt you and never gave up trying to find you.. Therefore… PLEASE CALM DOWN" Bonnie ran ahead and appealed to Zygarde earnestly..

Zygarde's face softened but it didn't relax. It's mind was torn between Squishy and Z2.

 **Zygarde's mind**

"She's right. She's my friend. They are innocent….." squishy thought

"How can you say so? They were going to kill Xerneas and Yveltal for the power of my cells. They've taken them to an unknown location, perhaps _already killed_ them. Will you _forgive_ the killers of our two fellow legendaries?!" z2 made a strong case.

"No, I will not but will you agree let the humans live if we find our two fellow safe and sound?" Squishy asked its another core z2.

"Very well" z2 agreed to the compromise. "If they bring Xerneas and Yveltal back right now, I shall pardon their kind. However if they _cannot_ produce them, I shall have my revenge and you shall not stop me. They can bring them back tomorrow by dawn."

The compromise was reached and communicated to Ash via telepathy.

 **Lysandre Lab again**

"Go Alain my dear fellow... You will never get a chance to beat Zygarde with your excellent mega charizard" Lysandre was dishevelled and now hiding in the ruins (the rockslide from explosion had flattened the bushes) but his greedy hope was still alive. _Yes Alain shall win then I can have the cells I want for ultimate power and Immortality. I can still fix this. It's NOT over. It can't be over._

"But why are you hidden here? I saw police on the other side. Why not cooperate with them?" Alain didn't know about Lysandre's greedy desires, nor did he know much about arrests of team flare. Alain walked into the ruined looking forward to a battle with the legendary pokemon when he was stopped in track by Professor Sycamore's shout.

"Alain! What are YOU doing now? Why did you betray my trust by making your services available to evil organization like team flare? What do you intend to do NOW?" Sycamore was earnest in his desperate queries.

"I'm here to challenge Zygarde to a pokemon battle." Alain answered.

"ALAIN! do you know what you're doing? Team Flare or Lysandre Lab as they're known, have threatened to kill Xerneas and Yveltal if Zygarde doesn't make Lysandre immortal and powerful!"

Sycamore yelled at him, grasping his collar.

"No. You're mistaken. My boss works for peace and plans to utilize the power of mega evolution for peaceful purpose. By working for him, I was able to challenge many powerful pokemon and train my charizard to be the best charizard of the world. " Alain's faith was unshaken.

"Alain. Professor Sycamore's right. Take a look around you. Does it look like peace to you? When you helped those guys kidnap squishy from us, was that peace according to you?! " Ash made their case by pointing at the collapsed hills and trees. It looked like a Tsunami had hit. "Zygarde doesn't trust humans now because of your boss. Lysandre has taken Xerneas and Yveltal to an unknown location and unless we can produce them safe and sound tomorrow by dawn, Zygarde will wipe human race out."

Alain was shocked... "But he told me he wanted to get a specific pokemon for research of mega evolution. I was simply helping them capture a pokemon for peaceful purpose."

"Alain, there's right and wrong in this world! You _never_ _hurt_ OR forcefully capture a pokemon, even if it's for peaceful purpose! You capture it by caring for it and winning its trust by showing you don't mean to hurt. I THOUGHT I TAUGHT YOU THAT! I TEACH IT EVERYONE WHO WORKS WITH POKEMON" Sycamore's face was contorted in rage while Alain now looked ashamed.

"You're right. Everyone, I'm sorry for what I have done." He bowed to his knees.

"Alain perhaps you can help us. We don't have much time. We have _got_ to find Xerneas and Yveltal and bring them to Zygarde by dawn. Do you know where they are? You worked for Lysandre." Ash called.

"No. He never let me get involved in lab. Now I see why." Alain lowered his head.

"What're we going to do?" Serena looked worryingly to Ash.

"If only we could sense them…"Ash said desperately. _wait a minute. SENSE them. Who have we seen do that? DIANTHA! When team rocket captured her Gardevoir, she and gardevoir sensed and found each other! It's a slim chance but it might just work!_

"Alain can you bring Diantha and her gardevoir to us, as soon as possible?" Ash exclaimed. The thought of having some hope was exciting for him.

"Certainly. My charizard flies faster than anyone. I shall have her here in couple of hours." He took off on his charizard.

"Officer, have you found where Xerneas and Yveltal are from team Flare members?" Ash turned to the officer.

"No. Nobody but Lysandre and Xerosic know where they're. Xerosic won't talk, he's sulking about his research. But we've found Lysandre himself hiding behind a rock. He talks about his plan but won't reveal where to find the pokemon. He says if he cannot be immortal, the world has no meaning for him." Officer shook his head.

"Right! So let's just search Lysandre's lab until Alain gets here with Diantha." Ash was a foolish kid most of the times, that is, he was _really_ dense about people's feelings but he was not the one to panic in face of danger.


	9. Zygarde's wrath 2 (final)

**A/N Thanks for sticking with me guys. You are awesome...Here's the final chapter! Enjoy :)**

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 **Two hours later… five hours until dawn**

"Hey look there's Diantha." Bonnie pointed from the window of the lab. A pretty lady in white short dress and cropped gray hair was being helped down by Alain from his Charizard.

"Alain has told me what happened. Where's Zygarde?" she didn't bother about niceties. Her deep gray eyes were tense and her voice of forced calm.

"It's where the team flare left it. We've six more hours to find Xerneas and Yveltal. Team flare won't reveal their location and Zygarde will trust humans again only if we present both the legendaries before it" Ash offered concise summary.

"Then we must find them. Is there a way to do it by dawn professor?" Diantha turned to professor Sycamore. He looked at Ash.

"This young man tells me you and your pokemon gardevoir can sense where each other are. Can you sense other pokemon?" Sycamore's voice was grave and everyone looked at Diantha, hanging onto her every word.

"I don't know. We've never had to sense anyone else…" The champion was worried. The task seemed impossible and the time short. _Find Xerneas and Yveltal from wherever they are_.

Ash had an idea. "The fairy aura. Xerneas has a fairy aura… Gardevoir is a psychic and fairy type…Can she try and sense the fairy aura?" He exclaimed.

"Please Diantha. You're our only hope." Serena's blue eyes were earnest.

"Well Ash, I will give it my best shot." Diantha was still uncertain but she took out her pokeball. "gardevoir, I need your assistance"

The elegant green and white humanoid pokemon materialized before them. "gar…devoir" she responded in her grave voice.

"Gardevoir, we need to find Xerneas and Yveltal. I want you to concentrate and sense Xerneas's fairy aura" The champion asked. There was only hope and determination in her expression. She never let her pokemon know how unsure or terrified she feels sometimes.

"Gar…devoir" The elegant pokemon closed her eyes and brought her slim green arms together. Her figure seemed to glow faint silver…

Few minutes passed. Ash had another brainwave. "Hey we once found Xerneas in Allearth forest! How about we go there and try this?"

"But how can we get to Allearth forest? We hardly have four more hours now!" Clemont scratched his head.

Diantha turned to him and actually smiled a little. "Relax Clemont. My gardevoir can teleport us there." She continued, "Since we don't seem to make much headway from here, how about we try where Ash says."

 **Allearth forest**

They stood eagerly in Allearth forest. Gardevoir's eyes were closed as she tried to feel fairy aura.

Finally, after what seemed ages later, she opened her eyes. Diantha didn't need words to understand her pokemon. They often communicated wordlessly and perfectly.

"She's found it. Well done Ash. If it wasn't for you and your smart thinking, it wouldn't have been possible." Ash was embarrassed at being complimented by the champion herself. Serena looked at him proudly, her heart beat faster.

"Oh thanks Diantha but your gardevoir was the one who did it". They all thanked gardevoir.

"Let's move. Gardevoir, teleport us to Xerneas." Gray haired Diantha was the one to act fast.

A strange sensation grasped them as they felt themselves appearing from one place into another.

As they saw the place, they saw why this was a perfect place for a secret base. The forest was completely isolated with no sign of life whatsoever and far away from all cities and towns.

A small building was protected by few grunts and their houndooms. Houndooms surrounded them supervised by grunts, ready to capture whoever that found their secret base.

"Greninja I choose you" Ash yelled before grunts had so much as moved a muscle.

Greninja took fighting stance as he noticed multiple opponents.

"Sylveon, come on out" A cute pink pokemon appeared from Serena's pokeball and wrapper her ribbon like feeler around Serena's hand. The ordinarily friendly pokemon's body tensed as she readied herself for a battle.

"Luxray.. Come out old friend" Clemont shouted then he whispered to the champion, "Diantha, please go and get Xerneas and Yveltal while we occupy the grunts." From the corner of his eyes, he saw her nod slightly.

Grunts weren't able to receive orders from their boss. Their communication system was broken by Zygarde's wrath in the Lumiose city nor did they know about Lysandre's arrest. Clemont decided to tell, "Listen to me. Team Flare in Lumiose city is finished. Each and every member has been arrested by the police. It would be better for you to surrender. You cannot win against us, especially since we're here with Kalos champion Diantha" He gestured to Diantha as he spoke.

Grunts were disbelieving about everything he said. One decided to call an attack.

"houndoom, flamethrower." A lasso of fire speeded towards Luxray.

"Luxray dodge" Luxray ducked out of way and the flamethrower hit houndoom behind him. The houndoom was annoyed by the attack, he growled and ran towards the first houndoom. Both grunts attention was diverted as they fought to get their pokemon under control. Clemont was excessively pleased with this development since he noticed Diantha and gardevoir teleport into the facility.

A lively battle was taking place on Ash's end.

"Greninja, water shuriken" two star shaped shuriken of water speeded towards the fire and dark type houndoom.

"FLAMETHROWER ON THAT SHURIKEN!" Grunt yelled. Houndoom's flamethrower evaporated the first shuriken, however the second one hit him right on head. Houndoon shrunk back as the water hit him when Ash called for cut.

A silver sword like shape materialized in Greninja's hands as he charged towards houndoom.

"Houndoom dark pulse NOW" Greninja didn't stop even as he was hit by purple and black dark pulse. Sword shined in the dark pulse and struck his opponent. But Greninja has tad taken damage from a direct hit up close. He looked at Ash and nodded.

Next, grunt was astonished as a giant tornado of water surrounded Greninja when he transformed into Ash-Greninja form. The water went as high as ten feet and spun like a tornado while greninja's body glowed and changed to resemble Ash. As the water resided, the water surrounding him became a huge star shaped, shining shuriken and rested itself on Greninja's back.

"Greninja, show them the fight is over. WATER SHURIKEN!" Ash shouted. Greninja moved so fast it was a blur. He took out that massive star shaped shuriken, aimed it at houndoom and fired straight. It was unstoppable by the dark pulse houndoom used. It hit houndoom through the dark pulse on his head and knocked him out.

Meanwhile Clemont and Serena were just about to finish their opponents. Both shouting encouragements to their pokemon.

"Very good Sylveon. Finish them off with your fairy wind." The houndoom on her end was blown away when a horizontal whirlpool of silver fairy wind hit him. The grunt ran away, just in case what the gym leader said about arrests had been true, he didn't want to be there anymore. _Only one grunt left._

Luxray had flinched when a houndoom had used dark type move bite on it. It was an after effect of the move. Grunt grabbed the chance to use dark pulse. Poor Luxray couldn't get out of the way in time.

"You can do it Luxray" Ash cheered which was echoed by Greninja, now back to his usual self.

"Go Clemont. Go Luxray" The blond haired Serena encouraged. Sylveon waved her ribbons in support.

"Thanks guys. Luxray are you okay?" Clemont didn't want to push him. "Luxxx" Luxray pulled himself up and poised to attack.

"Very good old friend. Shock your opponent with THUNDER" Clemont's shout was followed by a huge bolt of electricity that didn't stop at houndoom but paralyzed its trainer too. The grunt and his houndoom both fell down at once.

"All right! Way to go!" Ash and Serena cheered when Clemont smiled."Now lets go find Diantha.

"No need to find me. I'm right here." That voice belong to a pretty gray haired lady in short white dress. She was followed by Xerneas and Yveltal. "They were hurt by team flare but I have healed them. They know our situation and are ready to help us". She explained. One can't be the champion without knowing how to heal pokemon and Diantha had a gift of understanding their feelings and communicating hers. She had earned the trust of both the legendaries. They were all impressed and thanked her, Xerneas and Yveltal for everything.

"We still have… One hour left. Let's get a move on. Ready gardevoir?"

 **Lysandre Lab**

Zygarde was still in 80% form, not ready to trust humans yet. Squishy was anxious. It had the best time with Bonnie and wasn't willing to attack humans. However z2's case was strong and squishy could only hope Ash and his other friends bring back Xerneas and Yveltal in time.

Just then, with little sunrays behind their back, Ash, Clemont, Serena, Diantha walked into the garden with Shining Xerneas and broody Yveltal in front of them, the former walking elegantly, the latter floating. Zygarde was glad to see them safe and free.

Zygarde's cells started leaving his body as the sun rose. There was no need for the 80% form now. The condition was fulfilled. They had proved that not all humans were bad and it is not a mistake to trust.

Squishy jumped back in Bonnie's welcoming arms as z2 watched. It didn't say anything. Just turned transparent and vanished, to monitor the ecosystem it valued.

Xerneas took a good look at the destruction, the dead trees and flattened bushes were everywhere. It used geomancy. Rainbows of lights emitted from its body and flew in all directions, restoring life as they went. The trees stood back and the gardens bloomed again. Yveltal vanished towards the mountains somewhere to sleep.

As Zygarde and Yveltal returned to their own places, rainbows engulfed Xerneas one more time, covering it completely and blinding everyone. When they opened their eyes, there was a tall beautiful tree in front of them, some of its branches shaped like the legendary pokemon's antlers.

Everything was normal again, well, as normal it can be in the pokemon universe.

The end.


End file.
